3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

Cell

Volumn 135, Issue 5, 2008, Pages 919-932

  Wilusz, Jeremy E ^a   Freier, Susan M ^b   Spector, David L ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b ISIS PHARMACEUTICALS   (United States)

Author keywords

RNA

Indexed keywords

NUCLEAR RNA; NUCLEOTIDE; RNA POLYMERASE II; TRANSFER RNA; UNTRANSLATED RNA; RIBONUCLEASE; RIBONUCLEASE P; RNASE Z; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; DNA FLANKING REGION; ENZYME REGULATION; ENZYME SUBSTRATE; GENE LOCUS; GENETIC CODE; GENOMICS; HUMAN; HUMAN CELL; HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA SEQUENCE; TRANSCRIPTION INITIATION; AMINO ACID SEQUENCE; ANIMAL; CELL NUCLEUS; CYTOPLASM; GENETICS; HELA CELL; METABOLISM; MOLECULAR GENETICS; MOUSE; NEOPLASM; RNA PROCESSING; TUMOR CELL LINE;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CELL LINE, TUMOR; CELL NUCLEUS; CYTOPLASM; ENDORIBONUCLEASES; HELA CELLS; HUMANS; MICE; MOLECULAR SEQUENCE DATA; NEOPLASMS; RIBONUCLEASE P; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, TRANSFER; RNA, UNTRANSLATED;

EID: 56349113455     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2008.10.012     Document Type: Article

References (53)

1. Bass B.L. RNA editing by adenosine deaminaes that act on RNA. Annu. Rev. Biochem. 71 (2002) 817-846
2. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z., Snyder M., Dermitzakis E.T., Thurman R.E., et al. Identifcation and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
3. Braidotti G., Baubec T., Pauler F., Seidl C., Smrzka O., Stricker S., Yotova I., and Barlow D.P. The Air noncoding RNA: An imprinted cis-silencing transcript. Cold Spring Harb. Symp. Quant. Biol. 69 (2004) 55-66
4. Brennecke J., Aravin A.A., Stark A., Dus M., Kellis M., Sachidanandam R., and Hannon G.J. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128 (2007) 1089-1103
5. Cai X., and Cullen B.R. The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13 (2007) 313-316
6. Cai X., Hagedorn C.H., and Cullen B.R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as a mRNAs. RNA 10 (2004) 1957-1966
7. Carmell M.A., Girard A., van de Kant H.J., Bourc'his D., Bestor T.H., de Rooij D.G., and Hannon G.J. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12 (2007) 503-514
8. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., et al. The transcriptional landscape of the mammalian genome. Science 309 (2005) 1559-1563
9. Choi Y.H., and Hagedorn C.H. Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3′ poly(A) end phenotype. Proc. Natl. Acad. Sci. USA 100 (2003) 7033-7038
10. Colgan D.F., and Manley J.L. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11 (1997) 2755-2766
11. Conrad N.K., Mili S., Marshall E.L., Shu M.D., and Steitz J.A. Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element. Mol. Cell 24 (2006) 943-953
12. Costa F.F. Non-coding RNAs: New players in eukaryotic biology. Gene 357 (2005) 83-94
13. Davis I.J., His B., Arroyo J.D., Vargas S.O., Yeh Y.A., Motyckova G., Valencia P., Perez-Atayde A.R., Argani P., Ladanyi M., et al. Cloning of an alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation. Proc. Natl. Acad. Sci. USA 100 (2003) 6051-6056
14. de la Sierra-Gallay I.L., Pellegrini O., and Condon C. Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z. Nature 433 (2005) 657-661
15. Deng X., and Meller V.H. Non-coding RNA in fly dosage compensation. Trends Biochem. Sci. 31 (2006) 526-532
16. Dinger M.E., Mercer T.R., and Mattick J.S. RNA as extracellular signaling molecules. J. Mol. Endocrinol. 40 (2008) 151-159
17. Fantin V.R., Berardi M.J., Scorrano L., Korsmeyer S.J., and Leder P. A novel mitochondriotoxic small molecule that selectively inhibits tumor cell growth. Cancer Res. 2 (2002) 29-42
18. Fechter P., Rudinger-Thirion J., Florentz C., and Giegé R. Novel features in the tRNA-like world of plant viral RNAs. Cell. Mol. Life Sci. 58 (2001) 1547-1561
19. Filipowicz W., Bhattacharyya S.N., and Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight?. Nat. Rev. Genet. 9 (2008) 102-114
20. Ford L.P., Watson J., Keene J.D., and Wilusz J. ELAV proteins stabilize deadenylated intermediates in a novel in vitro mRNA deadenylation/degradation system. Genes Dev. 13 (1999) 188-201
21. Giegé R., Frugier M., and Rudinger J. tRNA mimics. Curr. Opin. Struct. Biol. 8 (1998) 286-293
22. Gopalan V., Vioque A., and Altman S. RNase P: Variations and uses. J. Biol. Chem. 277 (2002) 6759-6762
23. Gu H., Das Gupta J., and Schoenberg D.R. The poly(A)-limiting element is a conserved cis-acting sequence that regulates the length of poly(A) on nuclear pre-mRNAs. Proc. Natl. Acad. Sci. USA 96 (1999) 8943-8948
24. Gunawardane L.S., Saito K., Nishida K.M., Miyoshi K., Kawamura Y., Nagami T., Siomi H., and Siomi M.C. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315 (2007) 1587-1590
25. Hopper A.K., and Phizicky E.M. tRNA transfers to the limelight. Genes Dev. 17 (2003) 162-180
26. Hutchinson J.N., Ensminger A.W., Clemson C.M., Lynch C.R., Lawrence J.D., and Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8 (2007) 39
27. Jacobson M.R., Cao L.G., Taneja K., Singer R.H., Wang Y.L., and Pederson T. Nuclear domains of the RNA subunit of RNase P. J. Cell Sci. 110 (1997) 829-837
28. Ji P., Diedreichs S., Wang W., Boing S., Metzger R., Schneider P.M., Tidow N., Brandt B., Buerger H., Bulk E., et al. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22 (2003) 8031-8041
29. Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermuller J., Hofacker I.L., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316 (2007) 1484-1488
30. Kiss T., Fayet E., Jady B.E., Richard P., and Weber M. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb. Symp. Quant. Biol. 71 (2006) 407-417
31. Kuiper R.P., Schepens M., Thijssen J., van Asseldonk M., van den Berg E., Bridge J., Schuuring E., Schoenmakers E.F., and van Kessel A.G. Upregulation of the transcription factor TFEB in t(6;11)(p21;q13)-positive renal cell carcinomas due to promoter substitution. Hum. Mol. Genet. 12 (2003) 1661-1669
32. Lamond A.I., and Spector D.L. Nuclear speckles: A model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4 (2003) 605-612
33. Lau N.C., Lim L.P., Weinstein E.G., and Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294 (2001) 858-862
34. Lee Y., Kim M., Han J., Yeom K.H., Lee S., Baek S.H., and Kim V.N. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23 (2004) 4051-4060
35. Lin R., Maeda S., Liu C., Karin M., and Edington T.S. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 26 (2006) 851-858
36. Masui O., and Heard E. RNA and protein actors in X-chromosome inactivation. Cold Spring Harb. Symp. Quant. Biol. 71 (2006) 419-428
37. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
38. McKay R.A., Miraglia L.J., Cummins L.L., Owens S.R., Sasmor H., and Dean N.M. Characterization of a potent and specific class of antisense oligonucleotide inhibitor of protein kinase C-alpha expression. J. Biol. Chem. 274 (1999) 1715-1722
39. Mercer T.R., Dinger M.E., Sunkin S.M., Mehler M.F., and Mattick J.S. Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. USA 105 (2008) 716-721
40. Monia B.P., Lesnik E.A., Gonzalez C., Lima W.F., McGee D., Guinosso C.J., Kawasaki A.M., Cook P.D., and Freier S.M. Evaluation of 2′-modified oligonucleotides containing 2′-deoxy gaps as antisense inhibitors of gene expression. J. Biol. Chem. 268 (1993) 14514-14522
41. Peng J., Murray E.L., and Schoenberg D.R. The poly(A)-limiting element enhances mRNA accumulation by increasing the efficiency of pre-mRNA 3′ processing. RNA 11 (2005) 958-965
42. Prasanth K.V., and Spector D.L. Eukaryotic regulatory RNAs: An answer to the "genome" complexity conundrum. Genes Dev. 21 (2007) 11-42
43. Proudfoot N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16 (2004) 272-278
44. Rajaram V., Knezevich S., Bove K.E., Perry A., and Pfeifer J.D. DNA sequence of the translocation breakpoints in undifferentiated embryonal sarcoma arising in mesenchymal hamartoma of the liver harboring the t(11;19)(q11;q13.4) translocation. Genes Chromosomes Cancer 46 (2007) 508-513
45. Richter J.D. Cytoplasmic polyadenylation in development and beyond. Microbiol. Mol. Biol. Rev. 63 (1999) 446-456
46. Szymanski M., Barciszewska M.Z., Erdmann V.A., and Barciszewski J. A new frontier for molecular medicine: Noncoding RNAs. Biochim. Biophys. Acta 1756 (2005) 65-75
47. Topisirovic I., Culjkovic B., Cohen N., Perez J.M., Skrabanek L., and Borden K.L. The proline-rich homeodomain protein, PRH, is a tissue-specific inhibitor of eIF4E-dependent cyclin D1 mRNA transport and growth. EMBO J. 22 (2003) 689-703
48. Varshney U., Lee C., and RajBhandary U.L. Direct analysis of aminoacylation levels of tRNAs in vivo. J. Biol. Chem. 266 (1991) 24712-24718
49. Vasudevan S., Tong Y., and Steitz J.A. Switching from repression to activation: MicroRNAs can up-regulate translation. Science 318 (2007) 1931-1934
50. Vogel A., Schilling O., Spath B., and Marchfelder A. The tRNase Z family of proteins: Physiological functions, substrate specificity and structural properties. Biol. Chem. 386 (2005) 1253-1264
51. Weiner A.M., and Maizels N. tRNA-like structures tag the 3′ ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis. Proc. Natl. Acad. Sci. USA 84 (1987) 7383-7387
52. Zhao J., Hyman L., and Moore C. Formation of mRNA 3′ ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev. 63 (1999) 405-445
53. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415